Difference between revisions of "SDIWG:Meeting Minutes 20071116"
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[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]] | [[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]] | ||
| − | + | ==Notes== | |
''Friday, November 16, 2007: 2:30 -- 3:30 PM EST''<br> | ''Friday, November 16, 2007: 2:30 -- 3:30 PM EST''<br> | ||
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br> | ''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br> | ||
''[http://na-mic.org/Wiki/index.php/SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers SDIWG Meetings Page]''<br> | ''[http://na-mic.org/Wiki/index.php/SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers SDIWG Meetings Page]''<br> | ||
| − | <b>Save the date for the next SDWIG tcon/Connect, three months from now: Friday February 22, 2008< | + | <b>Save the date for the next SDWIG tcon/Connect, three months from now: Friday February 22, 2008</b> |
| − | + | ==TCon Agenda== | |
| − | * Roll Call/Note-taker (Ivo Dinov) (5 min) | + | *Roll Call/Note-taker (Ivo Dinov) (5 min) |
| + | *Minutes from most recent SDIWG tcon [[SDIWG:Meeting_Minutes_20070921|Sept 21, 2007]] (5 min) | ||
| + | *NCBC All Hand Meeting, 2008. Planning & Brainstorm discussion (Peter, Karin, All) | ||
| + | *Status check on two working groups: [[SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies|Biositemaps Resourceome]], [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]], [http://www.ncbcs.org/dbp_interactions.html NCBC Driving Biological Projects Interactions and Impact] | ||
| + | *NCBC Consortium authorship policies (Peter; Open Discussion with output a list of bullet ideas) | ||
| + | *CTSA Informatics Meeting in Chicago at AMIA (Brian, David, any others | ||
| + | present) | ||
| + | *Discuss AMIA/ISCB translational informatics summit in March, see [[Media:AMIA2008_NCBC_Paneldraft_v5.doc | Panel Draft]] | ||
| + | *Discussion of [[Media:Biositemaps-white-paper-v2.2.doc | Biositemaps white paper]] and of authorship (see more details in 'Appendix' below). | ||
| + | *Next 2 meeting dates set | ||
| + | *Questions/Information Sharing | ||
| − | + | <br> | |
| − | + | ==Appendix: Biositemaps white paper== | |
| − | + | *'''[[SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies|Biositemaps Resourceome]]''' (Ivo Dinov, Daniel Rubin, Will Schroeder, Beth Kirschner, Karen Skinner, Zohara Cohen, Bill Bug, Peter Lyster) | |
| − | + | **The biositemaps [[Media:Biositemaps-white-paper-v2.2.doc | white paper]] presents description of prototype for distributed architecture to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining software tools and information resources on the Internet. Each site which intends to contribute to the inventory instantiates a file on its Internet site ‘biositemap.xml’ which conforms to a defined schema and is tagged by a resource ontology. The prototype schema may be found at http://www.ncbcs.org/biositemaps/biositemaps-v04.xsd A good reference for XML editors is at http://en.wikipedia.org/wiki/Xml_editor e.g., we are using XMLmind. The prototype resource ontology may be found at http://bioontology.org/projects/ontologies/SoftwareOntology/ | |
| − | ** | + | **Further postings will be made at the NCBC portal at http://www.ncbcs.org/biositemaps/ |
| − | + | **TBD: Long-term plan for maintenance of schema and resource ontology (hosting, versioning, ownership,...). Converge on contents of schema and resource ontology with appropriate parties. This will amount to a v1.0 release (i.e., figure out where to stop now and leave extensions to a later date). Resolve issues of locating the biositemaps content (hard-wired, crawl,...) | |
| − | + | **Status of the NCBC iTools, which is uses the biositemaps. (production) http://www.loni.ucla.edu/iToolssvc/ncbc_iTools.html/http://iTools.loni.ucla.edu and (dev) http://netulla.loni.ucla.edu:8080/iToolssvc/ncbc_iTools.html/http://www.loni.ucla.edu/twiki/bin/view/CCB/iTools. | |
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| − | + | ==Minutes== | |
| − | Note taker: (Ivo Dinov) | + | Note taker: (Ivo Dinov) [Suggested order of note takers for future meetings: Dinov (this one); Chueh; Sherman; Schroeder; Floratos; Rubin; Jags] |
| + | *Review of [[SDIWG:Meeting_Minutes_20070921|Sept 21, 2007 Minutes]] | ||
| + | *Attendees: Dave Kennedy, Brian Athey, Suzy Lewis, Suzane Churchill, Jim Cavalcoli, Ivo Dinov, Jeanette Schmitte, Aris Floratos, Beth Kirshner, Joy Ku, Karen Skinner, Daniel Rubin, Karin Remington, David States, Jennie Larkin, Jags, Peter Lyster | ||
| + | *Go over dates for next year's meetings: | ||
| + | ** AMIA Summit on Translational Bioinformatics, San Francisco, http://www.amia.org/inside/releases/2007/translationalbioinformaticssummit_pr2007.pdf, March 10-12 2008 | ||
| + | ** Health Informatics April 11, 2008, Boston, MA - Health Informatics (Zak?) Need a link. | ||
| + | **NCBC All Hands Meeting, possible date June 30-July 2, Bethesda | ||
| + | *Peter went over the minutes of last meeting () | ||
| + | *Peter went over the agenda | ||
| + | *Peter will be away (dates?) | ||
| + | *AMIA 2008 panel - Brian presented the status (still pending but we should assume we all have to be there). | ||
| + | * Daniel/Brian/Others - ISCB/AMIA cross-over meeting? AMIA has two meetings (Spring/Fall). WG3 is leading this effort (URL). Link to proposal doc. Typo in doc... AMIA Meeting - March 10-12, 2008, Place? | ||
| + | *NCBC AHM 2008 - available dates (June 30-July 02, 2007)? | ||
| + | *Link NCBCs to CTSA's is important for success of the Roadmap. | ||
| + | *Karin - todays Roadmap retreat - busy summer schedule. | ||
| + | *Capacity of Lister Hill/NIH to house all NCBCs/reps/investigators for a NCBC AHM? | ||
| + | * Lister Hill works as there are break out rooms. | ||
| + | * Outreach sessions at NCBC AHM (dissemination events)? Karin was there in 2005 (spying!) | ||
| + | *7, 3 or 1 parallel sessions at AHM Dissemination events? Pros/Cons! | ||
| + | *How about wrapping around the 3 WGs (Jenny Larking and Bill/Gill ...) | ||
| + | *All NCBC reps should ping center PIs or email all PIs (may be better, Jenny, by next week). | ||
| + | * Morning session day 1 - dog-and-pony session; followed by working sessions of WGs and finally dissemination events (Peter). | ||
| + | * There is an enthusiasm among the PIs to get a collective NCBC AHM that provides functional connections and opportnities to echcange ideas. | ||
| + | * NCBC/Collab projects may be invited | ||
| + | * Mark - perhaps PIs should meet privately meet at AMIA to discuss programmatic issues. | ||
| + | * SDWGI meets once every 3 months 11:30 AM (Pacific), third Fri of the month. | ||
| + | * Tutorials for the Sci Ontology WG for the March AMIA meeting (Suzi?) | ||
| + | * Mark, Brian, ? had discussions on ontologies at the CTSA meeting | ||
| + | * Brian - proposal for a panel at the ISMB'08. Brian will email Suzan and Neal and take it further. | ||
| + | * Peter - update on the Chicago meeting. | ||
| + | * There are 7 WGs in the CTSA informatics consortium. Phone, face and ... for a set of recommendations that can be leverages in a paper discussion on clinical informatics. List that was agreed upon was clinical/aplied science (Brian)?!? How to tranlate to list to tranalational science endeavor. NCBCs need to be aware that the CTSA informatics group is really active. We need to synch with them and the NCRR has high expectations in the CTSA Informatics WG. | ||
| + | *Mark - programatic issues in creating NCBC/CTSA interactions. Instead of awaiting institution to get a CTSA award we need to bring them updated with NCBC progress. Invite them to NCBC AHM 2008. | ||
| + | * Page where all these meetings are listed? Peter - please make a link here (on top of SDWG site) | ||
| + | * Status of BioSiteMaps and iTools ... | ||
| + | * www.BioSiteMap.org domain purchased. | ||
| + | * White Paper authorship, clear aims, roles, technical blueprint? Consortium authorship? BISTI/NIH publication policies? Audience? | ||
| + | * iTools papers has explicit authorship list. | ||
| + | * White Paper (BioSiteMaps) Consortium Authorship of NCBCs. Future maintenance? Nature BioTech, as pub venue? | ||
| + | * Whether to perge iTools and BiositeMaps papers? All centers will have 1 contact person (center liaisons) send an email to Peter, Ivo and Daniel that you will provide comments back to us in 2 wks (by Dec. 01, 2007). Perhaps separate papers. | ||
| − | + | ==Action Items== | |
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Latest revision as of 21:17, 16 November 2007
Home < SDIWG:Meeting Minutes 20071116Agenda: NCBC Joint Working Group Meeting
Notes
Friday, November 16, 2007: 2:30 -- 3:30 PM EST
Please contact Peter Lyster for information Peter Lyster
SDIWG Meetings Page
Save the date for the next SDWIG tcon/Connect, three months from now: Friday February 22, 2008
TCon Agenda
- Roll Call/Note-taker (Ivo Dinov) (5 min)
- Minutes from most recent SDIWG tcon Sept 21, 2007 (5 min)
- NCBC All Hand Meeting, 2008. Planning & Brainstorm discussion (Peter, Karin, All)
- Status check on two working groups: Biositemaps Resourceome, Scientific Ontologies, NCBC Driving Biological Projects Interactions and Impact
- NCBC Consortium authorship policies (Peter; Open Discussion with output a list of bullet ideas)
- CTSA Informatics Meeting in Chicago at AMIA (Brian, David, any others
present)
- Discuss AMIA/ISCB translational informatics summit in March, see Panel Draft
- Discussion of Biositemaps white paper and of authorship (see more details in 'Appendix' below).
- Next 2 meeting dates set
- Questions/Information Sharing
Appendix: Biositemaps white paper
- Biositemaps Resourceome (Ivo Dinov, Daniel Rubin, Will Schroeder, Beth Kirschner, Karen Skinner, Zohara Cohen, Bill Bug, Peter Lyster)
- The biositemaps white paper presents description of prototype for distributed architecture to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining software tools and information resources on the Internet. Each site which intends to contribute to the inventory instantiates a file on its Internet site ‘biositemap.xml’ which conforms to a defined schema and is tagged by a resource ontology. The prototype schema may be found at http://www.ncbcs.org/biositemaps/biositemaps-v04.xsd A good reference for XML editors is at http://en.wikipedia.org/wiki/Xml_editor e.g., we are using XMLmind. The prototype resource ontology may be found at http://bioontology.org/projects/ontologies/SoftwareOntology/
- Further postings will be made at the NCBC portal at http://www.ncbcs.org/biositemaps/
- TBD: Long-term plan for maintenance of schema and resource ontology (hosting, versioning, ownership,...). Converge on contents of schema and resource ontology with appropriate parties. This will amount to a v1.0 release (i.e., figure out where to stop now and leave extensions to a later date). Resolve issues of locating the biositemaps content (hard-wired, crawl,...)
- Status of the NCBC iTools, which is uses the biositemaps. (production) http://www.loni.ucla.edu/iToolssvc/ncbc_iTools.html/http://iTools.loni.ucla.edu and (dev) http://netulla.loni.ucla.edu:8080/iToolssvc/ncbc_iTools.html/http://www.loni.ucla.edu/twiki/bin/view/CCB/iTools.
Minutes
Note taker: (Ivo Dinov) [Suggested order of note takers for future meetings: Dinov (this one); Chueh; Sherman; Schroeder; Floratos; Rubin; Jags]
- Review of Sept 21, 2007 Minutes
- Attendees: Dave Kennedy, Brian Athey, Suzy Lewis, Suzane Churchill, Jim Cavalcoli, Ivo Dinov, Jeanette Schmitte, Aris Floratos, Beth Kirshner, Joy Ku, Karen Skinner, Daniel Rubin, Karin Remington, David States, Jennie Larkin, Jags, Peter Lyster
- Go over dates for next year's meetings:
- AMIA Summit on Translational Bioinformatics, San Francisco, http://www.amia.org/inside/releases/2007/translationalbioinformaticssummit_pr2007.pdf, March 10-12 2008
- Health Informatics April 11, 2008, Boston, MA - Health Informatics (Zak?) Need a link.
- NCBC All Hands Meeting, possible date June 30-July 2, Bethesda
- Peter went over the minutes of last meeting ()
- Peter went over the agenda
- Peter will be away (dates?)
- AMIA 2008 panel - Brian presented the status (still pending but we should assume we all have to be there).
- Daniel/Brian/Others - ISCB/AMIA cross-over meeting? AMIA has two meetings (Spring/Fall). WG3 is leading this effort (URL). Link to proposal doc. Typo in doc... AMIA Meeting - March 10-12, 2008, Place?
- NCBC AHM 2008 - available dates (June 30-July 02, 2007)?
- Link NCBCs to CTSA's is important for success of the Roadmap.
- Karin - todays Roadmap retreat - busy summer schedule.
- Capacity of Lister Hill/NIH to house all NCBCs/reps/investigators for a NCBC AHM?
- Lister Hill works as there are break out rooms.
- Outreach sessions at NCBC AHM (dissemination events)? Karin was there in 2005 (spying!)
- 7, 3 or 1 parallel sessions at AHM Dissemination events? Pros/Cons!
- How about wrapping around the 3 WGs (Jenny Larking and Bill/Gill ...)
- All NCBC reps should ping center PIs or email all PIs (may be better, Jenny, by next week).
- Morning session day 1 - dog-and-pony session; followed by working sessions of WGs and finally dissemination events (Peter).
- There is an enthusiasm among the PIs to get a collective NCBC AHM that provides functional connections and opportnities to echcange ideas.
- NCBC/Collab projects may be invited
- Mark - perhaps PIs should meet privately meet at AMIA to discuss programmatic issues.
- SDWGI meets once every 3 months 11:30 AM (Pacific), third Fri of the month.
- Tutorials for the Sci Ontology WG for the March AMIA meeting (Suzi?)
- Mark, Brian, ? had discussions on ontologies at the CTSA meeting
- Brian - proposal for a panel at the ISMB'08. Brian will email Suzan and Neal and take it further.
- Peter - update on the Chicago meeting.
- There are 7 WGs in the CTSA informatics consortium. Phone, face and ... for a set of recommendations that can be leverages in a paper discussion on clinical informatics. List that was agreed upon was clinical/aplied science (Brian)?!? How to tranlate to list to tranalational science endeavor. NCBCs need to be aware that the CTSA informatics group is really active. We need to synch with them and the NCRR has high expectations in the CTSA Informatics WG.
- Mark - programatic issues in creating NCBC/CTSA interactions. Instead of awaiting institution to get a CTSA award we need to bring them updated with NCBC progress. Invite them to NCBC AHM 2008.
- Page where all these meetings are listed? Peter - please make a link here (on top of SDWG site)
- Status of BioSiteMaps and iTools ...
- www.BioSiteMap.org domain purchased.
- White Paper authorship, clear aims, roles, technical blueprint? Consortium authorship? BISTI/NIH publication policies? Audience?
- iTools papers has explicit authorship list.
- White Paper (BioSiteMaps) Consortium Authorship of NCBCs. Future maintenance? Nature BioTech, as pub venue?
- Whether to perge iTools and BiositeMaps papers? All centers will have 1 contact person (center liaisons) send an email to Peter, Ivo and Daniel that you will provide comments back to us in 2 wks (by Dec. 01, 2007). Perhaps separate papers.
